Various citrus types in cross section. Some of them are hybrids between two or more original species.
The botanical classification of the species, hybrids, varieties and cultivars belonging to the genus Citrus is called "citrus taxonomy".

Citrus taxonomy is complex.[1][2] Cultivated citrus are derived from various citrus species found in the wild. Some are only selections of the original wild types, while others are hybrids between two or more ancestors. Citrus plants hybridize easily between species with completely different morphologies, and similar-looking citrus fruits may have quite different ancestries.[3][4][5] Conversely, different-looking varieties may be nearly genetically identical, and differ only by a bud mutation.[6]

Interbreeding seems possible between all citrus plants, and between citrus plants and some plants which may or may not be categorized as citrus. The ability of citrus hybrids to self-pollinate and to reproduce sexually also helps create new varieties.

The hybrids of these four taxa include familiar citrus fruits like oranges, grapefruit, lemons, limes, and some tangerines.[1][12][13] In many cases, these crops are propagated asexually, and lose their characteristic traits if bred. However, some of these hybrids have interbred with one another and with the original taxa, making the citrus family tree a complicated network.

Because citrus taxonomy is still understudied[citation needed], there are many systems of classification that very often contradict each other. There are two main complete systems, that of Tanaka and that of Swingle; however, many citrus types were identified and named by individual taxonomists.

The basis of the "Tanaka system" is to provide a separate species name for each cultivar, regardless of whether it is pure or a hybrid of two or more species or varieties. Tanaka is therefore considered to have been a taxonomic "splitter".[15]

The "Swingle system" works differently, in that it first divides the genusCitrus into species, secondly divides it further into varieties, and lastly divides it again into cultivars or hybrids. The Swingle system is generally followed today with much modification; however, there are still huge differences in nomenclature between countries and even individual scientists.[16][17]

The same common names may be given to different citrus hybrids or mutations. Fruit with similar ancestry may be quite different in name and traits (e.g. grapefruit, common oranges, and ponkans, all pommelo-mandarin hybrids).

Note that many traditional citrus groups, such as true sweet oranges and lemons, seem to be bud sports, mutant descendants of a single hybrid ancestor.[11]

Mandarin oranges (tangerines, satsumas) are one of the basic species. Even pure-bred ones are genetically diverse. Many varieties commercially called mandarins are actually hybrids.[5][18] Most are hybrids with sweet oranges, but some are hybrids with lemons. Some are hybrids with pomelos (and thus like sweet oranges).

Citrus hybrids include many varieties and species that have been selected by plant breeders, usually for the useful characteristics of the fruit. Some citrus hybrids occurred naturally, and others have been deliberately created, either by cross pollination and selection among the progeny, or (rarely, and only recently) as somatic hybrids. The aim of plant breeding of hybrids is to use two or more different citrus varieties or species, in order to get intermediate traits, or the most desirable traits of the parents. In some cases, particularly with the natural hybrids, hybrid speciation has occurred, so the new plants are considered a different species from any of their parents. Citrus hybrid names are usually marked with a multiplication sign after the word "Citrus", for example Citrus × aurantifolia.

Citrus fruit taxonomy is still poorly understood, and even modern hybrids of known parentage are sold under general names that give little information about their ancestry, or technically incorrect information.[30][31]

Lemon and Lime: Most lemons are from one common ancestor, and diverged by mutation. The ancestor was a hybrid with citron, pummelo and mandarin ancestry; citrons contribute the largest share of the genome.[40]

The sweet lime, Citrus limettioides Tan. (syn. C. lumia Risso et Poit.), is often confused with the sweet lemon, C. limetta Tan., (q.v. under LEMON) which, in certain areas, is referred to as "sweet lime". In some of the literature, it is impossible to tell which fruit is under discussion.[43][44]

The same plant may also be known by different names:

The Indian sweet lime is the mitha nimbu (numerous modifications and other local names) of India, the limûn helou or succari of Egypt, and the Palestine sweet lime (to distinguish it from the Millsweet and Tunisian limettas, commonly called sweet limes).[45][46]

Citrofortunella according to the Swingle system, is a hybrid genus, containing intergeneric hybrids between members of the genusCitrus and the closely related Fortunella. It is named after its two parent genera. Such hybrids often combine the cold hardiness of the Fortunella, such as the Kumquat, with some edibility properties of the citrus species. Citrofortunellas, which are all hybrids, are marked with the multiplication sign before the word "Citrofortunella",[47] for example × Citrofortunella microcarpa or × Citrofortunella mitis which refer to the same plant.[48]

Carl Peter Thunberg originally classified the kumquats as Citrus japonica in his 1784 book, Flora Japonica. In 1915, Walter T. Swingle reclassified them in a segregate genus, Fortunella, named in honor of Robert Fortune. Seven species of Fortunella have generally been recognized—F. japonica, F. margarita, F. crassifolia, F. hindsii, F. obovata and F. polyandra, as well as the recently described F. bawangica. Since the kumquat is a cold hardy species, there are many hybrids between common citrus members and the kumquat (most popularly the calamondin that occurred naturally). Those hybrids are not citrus hybrids, according to Swingle, but reside in a separate hybrid genus which he called × Citrofortunella.

These plants are hardier and more compact than most citrus plants, often referred to as cold hardy citrus. They produce small acidic fruit and make good ornamental plants. Citrofortunella hybrids include:

Citrocirus also according to the Swingle system, is a hybrid genus, containing hybrids between members of the genusCitrus and the closely related Poncirus, which includes the trifoliate orange, a cold hardy plant that is commonly used as a citrus rootstock. Citrocirus commonly refers to the citranges which are hybrids between the trifoliate and sweet oranges. However a molecular investigation suggested that Fortunella, Citrofortunella, Poncirus and Citrocirus should all be equivocally included in the genus Citrus.[52][53]

The edible Australian limes are starting to be domesticated and commercially grown. Recent molecular research suggests that although Swingle placed them in the separate genera Microcitrus and Eremocitrus, they should also be included in the genus Citrus.[54]

Two additional genera, Triphasia and Clymenia, are likewise very closely related to the Citrus genus and bear hesperidium fruits, but they are not usually considered part of it. At least one, Clymenia, will hybridize with kumquats and some limes.